ESSENTIAL oils (EOs) as volatile products of plant secondary metabolism, possess significant antimicrobial activity, and have wide applications in the food industry and medicinal field. The purpose of this study focused on evaluating the antifungal properties of two commercial EOs, Chamomile (Chamomilla recutita L.) and Ginger (Zingiber officinale Roscoe). EOs were analyzed using gas chromatography-mass spectrometry (GC-MS). The most common compound identified in chamomile essential oil was α-bisabolol oxide A (49.09%) as a dominant compound, followed by En-yn-dicycloether (8.12%). The major compound of ginger essential oil was identified as isopulegol acetate (53.92%). The antimycotic potentiality of essential oils was detected in vitro by using agar disc diffusion method, microdilution assay for minimum inhibitory concentration (MIC) and minimum fungicidal concentration (MFC) against three pathogenic fungal strains, Penicillium chrysogenum, Aspergillus niger and Aspergillus flavus. The pathogenic strains were isolated from a stored seed-borne pathogen such as bean, popcorn, and rice. The results indicated that chamomile EO was the most effective extract and showed a potent antifungal activity against all the selected fungi when compared to ginger EO with maximum inhibition zone (5.15±0.07cm) against Penicillium chrysogenum. The minimum inhibitory concentration and minimum fungicidal concentration of the chamomile EO on the test fungi were in the range of 1.25-2.5μg/ml and 2.5–5.0μg/ml, respectively. Chamomile EO extract would be a suitable candidate for further research to validate its role in pharmaceutical applications and agricultural purposes for safe and eco-friendly seed-treatments.